[Chimera-users] writing translation/rotation

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 8 10:14:38 PDT 2007

Hi Thomas,
(1) Currently to transform one structure relative to another, they  
need to be in separate files, so first put chain A in one PDB file,  
chain B in another.

(2) Then, decide how to match (superimpose) the structures.  There  
are several options - MatchMaker (which will figure out the  
correspondences for you by doing a sequence alignment and then  
matching alpha-carbons), the "match" command which will allow you to  
name the specific atoms you want to use for fitting, both with or  
without fit iteration (pruning far-apart pairs from the fit). Usually  
the MatchMaker defaults, which include fit iteration, work quite well  
- thus I usually try those first.  (specific example below)  Make  
note of how the match was done once you are happy with it.

(3) Assuming you have rotated and translated things around in order  
to look at the match, you next want to reset to untransformed  
positions (at least of the A chain) and re-match with the approach  
worked out earlier.  Then write the matrices to a file or the Reply  
Log as desired.

Specific example:  PDB entry 1zik is a leucine zipper with A and B  
chains.  With text editing, I created zika.pdb (just the A chain) and  
zikb.pdb (just the B chain).
In chimera:
- open zika.pdb
- open zikb.pdb
command: mm #0 #1

(this is the command version of MatchMaker, using defaults and  
zika=#0 reference, zikb=#1 structure to match)  I decide this match  
looks good by rotating/translating and visual examination.  Then  
reset, re-match, write matrices.

command: reset     (now don't rotate/translate!)
command: mm #0 #1
command: matrixget -     (the "-" sends the info to the Reply Log.   
could also write to file)

Here is the info pasted from the Reply Log, which is under Favorites  
in the menu:
Model 0.0
	1 0 0 0
	0 1 0 0
	0 0 1 0
Model 1.0
	0.318155 -0.0547522 0.946456 7.3815
	0.0202055 -0.997713 -0.0645095 35.85
	0.947823 0.0396477 -0.316321 -9.44741

The "matrixget/matrixset" man page has more information on the matrices:

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 8, 2007, at 5:19 AM, Thomas C. Marlovits wrote:

> Hi,
> am looking for an analysis tool in Chimera  that would write out -  
> let's say a matrix for translation/rotation of a pdb-file in  
> respect to another one.
> Usage:  would like to align chain A and chain B present in a pdb- 
> file and want to know which translation/rotation matrix has to be  
> applied in order to convert  the non-aligned pdb-coordinates of  
> chain B to the 'new" aligned pdb-coordinates.
> Thanx for your help,
> -Thomas
> ---------------------------------------------------------------------- 
> ---------
> Thomas C. Marlovits, PhD, M.A.S.
> IMP-IMBA Research Center
> 	- Research Institute of Molecular Pathology (IMP)
> 	- Institute of Molecular Biotechnology, Austrian Academy of  
> Sciences (IMBA)
> Dr. Bohr-Gasse 3
> Room IMBA/6.02
> A-1030 Vienna
> Austria, Europe

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